Sir,
I have been referring some papers and in one of your papers you have
mentioned the use of ff99bsc0εζ OL1 forcefield( Rna-dna-protein hybrid if
I am right ) . So there OL15 was not mentioned which made me wonder what
is the difference on the same.
On 17 Sep 2020 14:17, "Jiri Sponer" <sponer.ncbr.muni.cz> wrote:
> Dear all,
>
> OL15 is the complete version.
>
> 1) It started from the ff99bsc0 version by adding DNA
> specific modification of chi (chiOL4, Krepl et al. JCTC 2012),
> important for example for quadruplexes. It is because it
> was necessary to split the RNA and DNA force fields
> due to contradicting requirements.
>
> 2) Then (Zgarbova et al JCTC 2013) eps/zeta has been modified,
> resolving the B-DNA helical twist and BI/BII (ezOL1).
>
> 3) Finally, (Zgarbova et al 2015 JCTC)
> the tricky beta dihedral (bOL1) has been reparametrized,
> which further improves B-DNA and is essential for Z-DNA. Simultaneously,
> to SIMPLIFY the name, it has been named
> as OL15, which includes all the earlier modifications.
> OL15 = Cornell et al. + ff99 + bsc0 + chiOL4 + ezOL1 + bOL1.
>
> Thus, OL15, as used, is basically a complete reparametrization
> of the dihedral potentials of the seminal Cornell et al.
> force field from 1995, published in a series of steps in 1999/2000, 2007,
> 2012, 2013, and 2015.
>
> It is explained in the Zgarbova et al paper JCTC 2015
> (Refinement of the SugarPhosphate Backbone Torsion Beta for
> AMBER Force Fields Improves the Description of Z- and BDNA)
> on p. 5724:
> "We introduce a shorthand OL15 for the
> combination of the bOL1, ezOL1 and chiOL4 dihedral modifications
> (named after the city of Olomouc, parametrization version
> 2015) ."
>
> So, OL15 includes everything.
>
> Best wishes, Jiri
>
> On Thu, 17 Sep 2020, David Cerutti wrote:
>
> Date: Thu, 17 Sep 2020 00:28:20 -0400
>> From: David Cerutti <dscerutti.gmail.com>
>> Reply-To: AMBER Mailing List <amber.ambermd.org>
>> To: AMBER Mailing List <amber.ambermd.org>
>> Subject: Re: [AMBER] Query on nucleic acid force fields
>>
>> I do not know what the special characters are in your titles there. I
>> have
>> listed for you the nucleic acid force fields that Amber offers as part of
>> its installation--OL15 is among them but I do not know about the ff99bsc
>> model. I have heard of something like this but you will need to look in
>> the directories I described to see if there are perhaps some hints in the
>> comments of those files. In leaprc.DNA.OL15, the preamble states:
>>
>> #
>> # ----- NOTE: this is designed for PDB format 3!
>> # Uses ff99bsc0+OL15 for DNA
>> # (ff99): Wang et al. J. Comp. Chem. 21: 1049, 2000
>> # (bsc0): Perez et al. Biophys J. 92: 3817, 2007
>> # (OL15): Zgarbova et al. JCTC 11: 5723, 2015
>> # load atom type hybridizations
>> #
>>
>> So there is definitely a component of ff99bsc0 in there, but I don't know
>> about the OL1 part you are talking about.
>>
>> Dave
>>
>>
>> On Thu, Sep 17, 2020 at 12:15 AM Jenny 148 <jenny.rs140.gmail.com> wrote:
>>
>> Sir,
>>> My major doubt is whether OL15 forcefield and ff99bsc0εζ OL1 forcefield
>>> are
>>> the same??
>>> On 17 Sep 2020 09:05, "David Cerutti" <dscerutti.gmail.com> wrote:
>>>
>>> In order to source a nucleic acids force field you will state, in your
>>>> leaprc, things like this:
>>>>
>>>> source leaprc.DNA.OL15
>>>> source leaprc.RNA.OL3
>>>>
>>>> For DNA< you have choices of bsc1 and OL15--I am almost certain that
>>>>
>>> those
>>>
>>>> are substantially different, but check the literature from Cheatham
>>>>
>>> group.
>>>
>>>> For RNA, you have LJbb, OL3, ROC, Shaw, and YIL options. I cannot
>>>> advise
>>>> you on one model or another in this respect, but look in each of the
>>>>
>>> leaprc
>>>
>>>> files (located in ${AMBERHOME}/dat/leap/cmd/leaprc.[RD]NA.(option), and
>>>> you
>>>> should see lines like "loadOff DNA.OL15.lib" and "parm10 =
>>>>
>>> loadAmberParams
>>>
>>>> parm10.dat." The latter tells it to use torsion parameters from parm10,
>>>> a
>>>> central collection of valence terms from our protein force fields. You
>>>> will find parm##.dat files in ${AMBERHOME}/dat/leap/parm/, and .lib
>>>> (library) files in ${AMBERHOME}/dat/leap/lib/.
>>>>
>>>> HTH,
>>>> Dave
>>>>
>>>>
>>>> On Wed, Sep 16, 2020 at 9:12 AM Jenny 148 <jenny.rs140.gmail.com>
>>>> wrote:
>>>>
>>>> Dear all,
>>>>> The question might be really trivial. I would like to know if the OL15
>>>>> forcefield and ff99bsc0εζ OL1 forcefield are the same. If not what is
>>>>>
>>>> the
>>>
>>>> difference. And how to source ff99bsc0εζ OL1? Thank you for your
>>>>>
>>>> time.
>>>
>>>>
>>>>> --
>>>>> Jenny R.S
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 17 2020 - 02:00:02 PDT
